I am working on some yeast strains and I am interested in INDELS. The bam files I have are the ones aligned with bowtie as aligner. I ran GATK pipeline for calling snps and INDELS using Unified genotyper but I did not get any INDELS in my vcf file produced. Doing some research as to why I am not getting any INDELS, I came across this post
One of the comments says
"I think it's important to note that BWA is one of the few fast mapping algorithms that allows for indels. Tools like Maq and Bowtie will not map reads if there is an insertion or deletion. I have used BWA to map 75bp Illumina reads at 20x coverage to a 30Mb fungal genome with good results."
So I went back to my bam files and tried to query the CIGAR string for I or D but didn't found anything. Does this mean bowtie won't report any reads where insertion or deletion is taking place.
Also I want to know that software's which calls for INDELS uses cigar string to tell whether INDELS are present or not or they use completely different approach?? Because If they make use of CIGAR string from bam file then it is easy to look for INDELS just in the bam file though a vcf file is more appropriate for obvious reasons like more detailed explanation.
So if bowtie does not report INDELS should i use bwa to align my reads and then look for INDELS.
Hope to hear from you soon.